|
| Status |
Public on Oct 11, 2022 |
| Title |
Wildtype-control-1 |
| Sample type |
SRA |
| |
|
| Source name |
BY4741
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell line: BY4741
genotype: WT
treatment: no
|
| Treatment protocol |
Cells were untreated or treated with 50 mM caffeine for 1h
|
| Growth protocol |
Yeast cell cultures and treatments with caffeine were performed in YEPD (1% yeast extract, 2% peptone, and 2% dextrose) or minimal SD media supplemented with the required amino acids.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
WT no treatment
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to sacCer3 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: sacCer3
Supplementary files format and content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Oct 06, 2022 |
| Last update date |
Oct 12, 2022 |
| Contact name |
Woo-Hyun Chung |
| Organization name |
Duksung Women's University
|
| Street address |
Samyangro 144-gil 33, Dobonggu
|
| City |
Seoul |
| ZIP/Postal code |
01369 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE214902 |
Yap1-mediated Flr1 expression reveals crosstalk between oxidative stress signaling and caffeine resistance in Saccharomyces cerevisiae |
|
| Relations |
| BioSample |
SAMN31181805 |
| SRA |
SRX17812334 |
